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Using NMR and MD simulation to study helicity in IDPs - News-Medical.net
Sep 15, 2017 - 2:17 AM - by nmrlearner
nmrlearner's Avatar
News-Medical.net


Using NMR and MD simulation to study helicity in IDPs
News-Medical.net
Particularly when combined with techniques such as nuclear magnetic resonance (NMR) spectroscopy, these studies allow atomistic understanding of the various conformations proteins adopt. One of the main techniques for modeling proteins is molecular ...

and more »

Using NMR and MD simulation... [Read More]
0 Replies | 64 Views
[NMR] Nobel Prize winner Nico Bloembergen passed away at age 97
Sep 15, 2017 - 2:17 AM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

[NMR] Nobel Prize winner Nico Bloembergen passed away at age 97



From the Ampere Magnetic Resonance List:


Dear colleagues,


Last week, Nobel laureate Professor Nicolaas Bloembergen, a pioneer in the field of NMR and laser spectroscopy passed away at age of 97. As an undergraduate Bloembergen studied Physics at Utrecht University from 1938 to 1943 and received his PhD in Physics from Leiden University with C.J. Gorter in 1948 on the topic of Nuclear Magnetic Relaxation. His thesis resulted in the famous BPP (Bloembergen, Purcell and Pound) paper which still serves as a point of departure for understanding many NMR relaxation experiments. In 1973 he returned to Leiden and occupied the Lorentz Chair in Physics. In 1981, he was awarded the Nobel Prize in Physics for his work in coherent optics. In 2001 in honour of his achievements, the NMR group at Utrecht University named their laboratory the Bloembergen Building.


For further information on a true scientific giant, please look out for an obituary written by C. Luchinat, R. Boelens, and R. Kaptein that will appear on the Ampere website and in the Ampere newsletter soon.


Also, please see, for example:
https://www.uu.nl/en/news/uu-alumnus...en-passed-away
... [Read More]
0 Replies | 45 Views
Pressure dependence of side chain 13 C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2
Sep 14, 2017 - 11:59 AM - by nmrlearner
nmrlearner's Avatar Pressure dependence of side chain 13 C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH 2

Abstract

For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200┬*MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For HN, N and C╬▒ the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.



... [Read More]
0 Replies | 21 Views
[NMR paper] Whole Ribosome NMR: Dipolar Couplings and Contributions to Whole Cells.
Sep 14, 2017 - 11:59 AM - by nmrlearner
nmrlearner's Avatar Whole Ribosome NMR: Dipolar Couplings and Contributions to Whole Cells.

Related Articles Whole Ribosome NMR: Dipolar Couplings and Contributions to Whole Cells.

J Phys Chem B. 2017 Sep 13;:

Authors: Nygaard R, Romaniuk JAH, Rice DM, Cegelski L

Abstract
Solid-state NMR is a powerful tool for quantifying chemical composition and structure in complex assemblies and even whole cells. We employed N{P} REDOR NMR to obtain atomic-level distance propensities in intact 15N-labeled E. coli ribosomes. The experimental REDOR dephasing of shift-resolved lysyl amine nitrogens by phosphorous was comparable to that expected from a calculation of N-P distances involving the lysines included in the crystal structure coordinates. Among the nitrogen contributions to the REDOR spectra, the strongest dephasing emerged from the dipolar couplings to phosphorous involving nitrogen peaks ascribed primarily to rRNA and the weakest dephasing arose from protein amide nitrogens. This approach is applicable to any macromolecular system and provides quantitative comparisons of distance proximities between shift-resolved nuclei of one type and heteronuclear dephasing spins. Enhanced molecular specificity could be achieved through the use of spectroscopic filters or specific labeling. Furthermore, ribosome 13C and 15N CPMAS spectra were compared with those of whole cells from which the ribosomes were isolated. Whole-cell signatures of ribosomes were identified and should be of value in comparing... [Read More]
0 Replies | 21 Views
[NMR paper] Gradient reconstitution of membrane proteins for solid-state NMR studies.
Sep 14, 2017 - 11:59 AM - by nmrlearner
nmrlearner's Avatar Gradient reconstitution of membrane proteins for solid-state NMR studies.

Related Articles Gradient reconstitution of membrane proteins for solid-state NMR studies.

J Biomol NMR. 2017 Sep 12;:

Authors: Lacabanne D, Lends A, Danis C, Kunert B, Fogeron ML, Jirasko V, Chuilon C, Lecoq L, Orelle C, Chaptal V, Falson P, Jault JM, Meier BH, B÷ckmann A

Abstract
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR. NMR spectra recorded on a sample produced by GRecon showed a highly similar fingerprint as those recorded previously on samples reconstituted by dialysis. GRecon sample preparation presents a gain in time of nearly an order of magnitude for reconstitution, and shall represent a valuable alternative in solid-state NMR membrane protein sample preparation.
... [Read More]
0 Replies | 26 Views
[NMR paper] Distribution of amyloid-like and oligomeric species from protein aggregation kinetics
Sep 14, 2017 - 11:59 AM - by nmrlearner
nmrlearner's Avatar Distribution of amyloid-like and oligomeric species from protein aggregation kinetics


Amyloid fibrils and soluble oligomers are two types of protein aggregates associated with neurodegeneration. Classic therapeutic strategies try to prevent the nucleation and spread of amyloid fibrils, whilst diffusible oligomers have emerged as promising drug targets affecting downstream pathogenic processes. We developed a generic protein aggregation model and validate it against measured compositions of fibrillar and non-fibrillar assemblies of ataxin-3, a protein implicated in Machado-Joseph disease. The derived analytic rate-law equations can be used to (i) identify the presence of parallel aggregation pathways and (ii) estimate the critical sizes of amyloid fibrils. The discretized population balance supporting our model is the first to quantitatively fit time-resolved measurements of size and composition of both amyloid-like and oligomeric species. The new theoretical framework can be used to screen a new class of drugs specifically targeting toxic oligomers.

More...
0 Replies | 30 Views
[NMR paper] Laser-initiated Radical Trifluoromethylation of Peptides and Proteins and Its Application to Mass Spectrometry-Based Protein Footprinting
Sep 13, 2017 - 8:48 PM - by nmrlearner
nmrlearner's Avatar Laser-initiated Radical Trifluoromethylation of Peptides and Proteins and Its Application to Mass Spectrometry-Based Protein Footprinting


We describe a novel, laser-initiated radical trifluoromethylation for protein footprinting and establish its broad residue coverage. *CF3 reacts with 18 of 20 common amino acids including Gly, Ala, Ser, Thr, Asp, Glu that are relatively "silent" with *OH. This new approach to footprinting is a bridge between trifluoromethylation in materials and medicinal chemistry and structural biology and biotechnology. Its application to a membrane protein and to myoglobin show that the approach is sensitive to protein conformational change and solvent accessibility.

More...
0 Replies | 32 Views
Single-scan 13C diffusion-ordered NMR spectroscopy of DNP-hyperpolarised substrates #DNPNMR
Sep 13, 2017 - 8:48 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Single-scan 13C diffusion-ordered NMR spectroscopy of DNP-hyperpolarised substrates #DNPNMR

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Guduff, L., et al., Single-scan 13C diffusion-ordered NMR spectroscopy of DNP-hyperpolarised substrates. Chemistry, 2017: p. n/a-n/a.


https://www.ncbi.nlm.nih.gov/pubmed/28857281


Diffusion-ordered NMR spectroscopy (DOSY) is a powerful approach for the analysis of molecular mixtures, yet its application range is limited by the relatively low sensitivity of NMR. We show here that spectrally resolved 13C DOSY data can be collected, in a single scan, for substrates hyperpolarised by dissolution dynamic nuclear polarisation (D-DNP), which provides signal enhancements of several orders of magnitude. For this we use a convection-compensation pulse scheme, which we also analyse by numerical simulation. The proposed method further allows the acquisition of several consecutive DOSY spectra in a single D-DNP experiment.
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Go to The DNP-NMR Blog for more info.
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